| from collections import Counter |
| import datetime |
| from dateutil.parser import parse as dparse |
| import errno |
| import numpy as np |
| import os |
| import random |
| import sys |
| import time |
| import warnings |
| from Bio import pairwise2 |
| from Bio import BiopythonWarning |
| warnings.simplefilter('ignore', BiopythonWarning) |
| from Bio import Seq, SeqIO |
|
|
|
|
| np.random.seed(1) |
| random.seed(1) |
|
|
| AAs = [ |
| 'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', |
| 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y', |
| ] |
|
|
| def tprint(string): |
| string = str(string) |
| sys.stdout.write(str(datetime.datetime.now()) + ' | ') |
| sys.stdout.write(string + '\n') |
| sys.stdout.flush() |
|
|
| def mkdir_p(path): |
| try: |
| os.makedirs(path) |
| except OSError as exc: |
| if exc.errno == errno.EEXIST and os.path.isdir(path): |
| pass |
| else: |
| raise |
| |
| def deep_mutational_scan(sequence, exclude_noop=True): |
| for pos, wt in enumerate(sequence): |
| for mt in AAs: |
| if exclude_noop and wt == mt: |
| continue |
| yield (pos, wt, mt) |
|
|
|
|
| def make_mutations(seq, mutations): |
| mut_seq = [ char for char in seq ] |
| for mutation in mutations: |
| wt, pos, mt = mutation[0], int(mutation[1:-1]) - 1, mutation[-1] |
| assert(seq[pos] == wt) |
| mut_seq[pos] = mt |
| mut_seq = ''.join(mut_seq).replace('-', '') |
| return mut_seq |
|
|
| def find_mutations(seq1, seq2): |
| alignment = pairwise2.align.globalms( |
| seq1, seq2, 5, -4, -6, -.1, one_alignment_only=True, |
| )[0] |
|
|
| mutation_set = [] |
| pos1, pos2, pos_map = 0, 0, {} |
| for wt, mt in zip(alignment[0], alignment[1]): |
| if wt != '-': |
| pos1 += 1 |
| if mt != '-': |
| pos2 += 1 |
| if wt != mt and wt != '-' and mt != '-': |
| mut_str = f'{wt}{pos1}{mt}' |
| mutation_set.append(mut_str) |
|
|
| return mutation_set |
